def print_events(self, node):
"""Prints the events that occur on a node"""
print "-" * 20
print "%s (%.3f sub/site):" % (node.name, node.dist),
if self.events:
if self.events[node] == "dup":
print "duplication"
elif self.events[node] == "spec":
print "speciation"
elif self.events[node] == "gene":
print "extant"
losses = util.groupby(lambda x: x[0], self.losses)
if node in losses:
print len(losses[node]), "gene losses"
for i, (node, schild) in enumerate(losses[node]):
print "loss %d in species %s" % (i+1, str(schild.name))
for sleaf in schild.leaf_names():
print " %s" % sleaf
else:
print "no reconciliation available"
def draw_matches(self, sp, chrom, start, end, drawn=None):
vis = []
if drawn is None:
drawn = set()
# build list of matches in order of drawing
for gene in iter_chrom(self.db.get_regions(sp, chrom), start, end):
# need to sort matches by genome order so that mult-genome synteny
# is drawn top-down
# get orthologs
genes2 = [x for x in self.orth_lookup.get(gene.data["ID"], [])
if x in self.region_layout]
if len(genes2) == 0:
continue
rows = util.groupby(lambda x: self.region_layout[x].y, genes2)
keys = util.sort(rows.keys(), reverse=True)
rows = util.mget(rows, keys)
l = self.region_layout
for i in range(1, len(rows)):
for botGene in rows[i]:
gene1 = self.db.get_region(botGene)
for topGene in rows[i-1]:
if (botGene, topGene) in drawn:
continue
drawn.add((botGene, topGene))
gene2 = self.db.get_region(topGene)
y1 = l[topGene].y
y2 = l[botGene].y + 1
x1 = l[topGene].x
x2 = l[topGene].x + gene2.length()
x3 = l[botGene].x + gene1.length()
x4 = l[botGene].x
if self.fat_matches:
vis.append(quads(
self.colors["matches"],
x1, y1,
x2, y1,
x3, y2,
x4, y2))
vis.append(lines(self.colors["matches"],
x1, y1,
x4, y2))
return group(* vis)
def draw_matches(self, sp, chrom, start, end, drawn=None):
vis = []
if drawn is None:
drawn = set()
# build list of matches in order of drawing
for gene in iter_chrom(self.db.get_regions(sp, chrom), start, end):
# need to sort matches by genome order so that mult-genome synteny
# is drawn top-down
# get orthologs
genes2 = [
x for x in self.orth_lookup.get(gene.data["ID"], [])
if x in self.region_layout
]
if len(genes2) == 0:
continue
rows = util.groupby(lambda x: self.region_layout[x].y, genes2)
keys = util.sort(rows.keys(), reverse=True)
rows = util.mget(rows, keys)
l = self.region_layout
for i in range(1, len(rows)):
for botGene in rows[i]:
gene1 = self.db.get_region(botGene)
for topGene in rows[i - 1]:
if (botGene, topGene) in drawn:
continue
drawn.add((botGene, topGene))
gene2 = self.db.get_region(topGene)
y1 = l[topGene].y
y2 = l[botGene].y + 1
x1 = l[topGene].x
x2 = l[topGene].x + gene2.length()
x3 = l[botGene].x + gene1.length()
x4 = l[botGene].x
if self.fat_matches:
vis.append(
quads(self.colors["matches"], x1, y1, x2, y1,
x3, y2, x4, y2))
vis.append(
lines(self.colors["matches"], x1, y1, x4, y2))
return group(*vis)
def makeFamilyGeneNames(self):
"""Tries to name and describe a family using its genes"""
self.cur.execute("""SELECT g.famid, g.common_name, g.description
FROM Genes g
""")
fams = util.groupby(lambda x: x[0], self.cur)
familyGeneNames = {}
for famid, rows in fams.iteritems():
names = util.unique([
"".join([i for i in x if not i.isdigit() and i != "-"])
for x in util.cget(rows, 1) if x != ""
])
names.sort()
description = self.getFamDescription(util.cget(rows, 2))
familyGeneNames[famid] = (",".join(names), description)
return familyGeneNames
def makeFamilyGeneNames(self):
"""Tries to name and describe a family using its genes"""
self.cur.execute("""SELECT g.famid, g.common_name, g.description
FROM Genes g
""")
fams = util.groupby(lambda x: x[0], self.cur)
familyGeneNames = {}
for famid, rows in fams.iteritems():
names = util.unique(["".join([i for i in x
if not i.isdigit() and i != "-"])
for x in util.cget(rows, 1)
if x != ""])
names.sort()
description = self.getFamDescription(util.cget(rows, 2))
familyGeneNames[famid] = (",".join(names), description)
return familyGeneNames
